Genome biology of long non-coding RNAs in humans: a virtual karyotype DOI Creative Commons
Alessandro Palma, Giulia Buonaiuto, Monica Ballarino

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 24, 2024

Abstract Background Long non-coding RNAs (lncRNAs) represent a unique and groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue cellular specificities. Although the number identified functional lncRNAs is increasing, comprehensive profiling lncRNA genomics remains elusive. Creating virtual karyotype especially important for species whose intrinsic features enable their biosynthesis function in context-dependent manners. Results conclusions To address this challenge, we employed existing annotation files to create statistical portrait genes comparison protein-coding genes. We provide foundational reference exploring genome, offering insights into genomic characteristics may enhance understanding biological significance impact.

Язык: Английский

Genome biology of long non-coding RNAs in humans: a virtual karyotype DOI Creative Commons
A. Palma, Giulia Buonaiuto, Monica Ballarino

и другие.

Computational and Structural Biotechnology Journal, Год журнала: 2025, Номер 27, С. 575 - 584

Опубликована: Янв. 1, 2025

Язык: Английский

Процитировано

0
The Relevance of the Accurate Annotation of Micro and Long Non-Coding RNA Interactions for the Development of Therapies DOI Open Access
Simona Panni

Genes, Год журнала: 2025, Номер 16(3), С. 262 - 262

Опубликована: Фев. 24, 2025

A large fraction of the human genome is transcribed in RNA molecules that do not encode for proteins but have a crucial role regulating almost every level gene expression and, thus, define specific phenotype each cell. These non-coding RNAs include well-characterized microRNAs and thousands less-defined longer transcripts, named long RNAs. Both types markedly affect onset progression numerous pathologies, ranging from cancer to vascular neuro-degenerative diseases. In recent years, substantial effort has been made design drugs targeting ncRNAs, promising advancements produced micro-RNA mimics inhibitors. Each ncRNA controls several targets, overall effect its inhibition or overexpression depends on function set genes it regulates. Therefore, selecting most appropriate target, predicting final outcome ncRNA-based therapies, utilize detailed accurate knowledge their functional interactions. this review, I recapitulate principal resources which collect information microRNA lncRNA networks, focusing non-homogeneity data result disparate approaches. highlight identifiers interaction evidence standardization helping user filter integrate derived different databases reliable web regulative relations.

Язык: Английский

Процитировано

0
Recent advances in investigation of circRNA/lncRNA-miRNA-mRNA networks through RNA sequencing data analysis DOI Creative Commons

Yulan Gao,

Konii Takenaka,

Si-Mei Xu

и другие.

Briefings in Functional Genomics, Год журнала: 2025, Номер 24

Опубликована: Янв. 1, 2025

Abstract Non-coding RNAs (ncRNAs) are RNA molecules that transcribed from DNA but not translated into proteins. Studies over the past decades have revealed ncRNAs can be classified small RNAs, long non-coding and circular by genomic size structure. Accumulated evidences eludicated critical roles of these transcripts in regulating gene expression through transcription translation, thereby shaping cellular function disease pathogenesis. Notably, recent studies investigated as competitive endogenous (ceRNAs) sequester miRNAs modulate mRNAs expression. The ceRNAs network emerges a pivotal regulatory function, with significant implications various diseases such cancer neurodegenerative disease. Therefore, we highlighted multiple bioinformatics tools databases aim to predict interaction. Furthermore, discussed limitations using current technologies potential improvement for detection. Understanding dynamic interplay within may advance biological comprehension, well providing targets therapeutic intervention.

Язык: Английский

Процитировано

0
Cut from the same cloth: RNAs transcribed from regulatory elements DOI
Ekaterina M. Stasevich,

Anna Šimonová,

Е. А. Богомолова

и другие.

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Год журнала: 2024, Номер 1867(3), С. 195049 - 195049

Опубликована: Июль 3, 2024

Язык: Английский

Процитировано

2
Update on functional analysis of long non-coding RNAs in common crops DOI Creative Commons
Aijing Zhang,

Wenxuan Pi,

Yashuo Wang

и другие.

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Май 30, 2024

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes extensively investigated animals, there has considerably less research on plant lncRNAs. Nevertheless, multiple studies major crops showed lncRNAs involved crucial processes, growth and development, reproduction, stress responses. This review summarizes progress lncRNA roles several crops, presents key strategies for exploring discusses current challenges future prospects. The insights provided this will enhance our comprehension of functions with potential implications improving crop genetics breeding.

Язык: Английский

Процитировано

1
Pivotal Role of miRNA–lncRNA Interactions in Human Diseases DOI

Farkhondeh Pooresmaeil,

Seifollah Azadi,

Behnam Hasannejad-Asl

и другие.

Molecular Biotechnology, Год журнала: 2024, Номер unknown

Опубликована: Дек. 13, 2024

Язык: Английский

Процитировано

1
Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis DOI Creative Commons
Alessandro Palma, Monica Ballarino

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 19, 2024

Abstract Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease for which comprehensive knowledge about the pathological mechanisms still lacking. A multitude of dysregulated cellular processes and pathways have been linked to ALS so far, including recent focus directed toward implication several classes non-coding (nc)RNAs. Within this context, class long ncRNAs (lncRNAs), may provide an important contribution onset severity pathogenesis, due their high tissue specificity function as gene expression regulators. Nevertheless, identification in humans often relies on differential analyses from bulk RNA-seq, limits targeting contexts where they be primarily involved. Here we apply dedicated pipelines single-nucleus nuclei datasets study lncRNA non-pathological pre-frontal human cortex. We found that brain, distinct cell subtypes express very different pattern lncRNAs suggest possible roles patients. Moreover, show involvement regulatory networks result differentially regulated conditions dissect genomic organization expressed lncRNAs.

Язык: Английский

Процитировано

0
Genome biology of long non-coding RNAs in humans: a virtual karyotype DOI Creative Commons
Alessandro Palma, Giulia Buonaiuto, Monica Ballarino

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Сен. 24, 2024

Abstract Background Long non-coding RNAs (lncRNAs) represent a unique and groundbreaking class of RNA molecules that exert regulatory functions with remarkable tissue cellular specificities. Although the number identified functional lncRNAs is increasing, comprehensive profiling lncRNA genomics remains elusive. Creating virtual karyotype especially important for species whose intrinsic features enable their biosynthesis function in context-dependent manners. Results conclusions To address this challenge, we employed existing annotation files to create statistical portrait genes comparison protein-coding genes. We provide foundational reference exploring genome, offering insights into genomic characteristics may enhance understanding biological significance impact.

Язык: Английский

Процитировано

0